Analysis
## Loading required package: plyr
##
## Attaching package: 'igraph'
## The following objects are masked from 'package:flowCore':
##
## normalize, parent, tree
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
## The following object is masked from 'package:base':
##
## union
## Compensation is applied on ~/temp/fcs/2016-05-20_PANEL 2_ZF_panel 2_F1632217_009.fcs
## Run Rphenograph starts:
## -Input data of 43333 rows and 9 columns
## -k is set to 11
## Finding nearest neighbors...DONE ~ 9.043 s
## Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 2.074 s
## Build undirected graph from the weighted links...DONE ~ 1.118 s
## Run louvain clustering on the graph ...DONE ~ 1.272 s
## Run Rphenograph DONE, totally takes 13.507s.
## Return a community class
## -Modularity value: 0.8305925
## -Number of clusters: 30 Runing t-SNE...with seed 42 DONE
Starting from PBMCs, I think
TSNE results

TSNE results, colored by Phenograph clusters detected

TSNE results, colored by manual gates

TSNE results, Manually gated

Starting from Dendritic cells,Natural killer cells, Monocytes, I think
TSNE results

TSNE results, colored by Phenograph clusters detected

TSNE results, colored by manual gates

TSNE results, Manually gated
